<div dir="ltr">Hi Chao,<div><div>I checked the tif file and just found the file information like this:</div><div>Horizontal resolution 300 dpi</div><div>Vertical resolution 300 dpi</div><div>dimensions 1916*1536</div><div>bit depth 16</div></div><div><br></div><div>So it means that before the reconstruction, i should use some tool to convert the projections images from 300dpi to 200dpi???</div><div>Best </div><div>Guangming</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><font style="line-height:23.32400131225586px" face="arial, helvetica, sans-serif" color="#674ea7"><b><i>Guangming Zang (Alex)</i></b></font><div style="line-height:23.32400131225586px"><font face="arial, helvetica, sans-serif"><b><i><font color="#0b5394">King Abdullah University of Science and Technology</font><font color="#073763">(KAUST)</font></i></b></font></div><div style="line-height:23.32400131225586px"><span style="font-family:arial;font-size:13px;line-height:20.020000457763672px"><font color="#0b5394"><b><i>University of Chinese Academy of Sciences(UCAS)</i></b></font></span><font face="arial, helvetica, sans-serif"><b><i><font color="#073763"><br></font></i></b></font></div><div style="line-height:23.32400131225586px"><br></div></div></div></div>
<br><div class="gmail_quote">2014-11-21 2:40 GMT+03:00 Guangming Zang <span dir="ltr"><<a href="mailto:guangming.zang@kaust.edu.sa" target="_blank">guangming.zang@kaust.edu.sa</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Chao,<div>thanks very much for your help.</div><div>I will try this command now. Result will be given later.</div><div>Thanks again for your generous help and valuable time.</div><div>Another question is , how to visual the large volume effectively?? 3D slicer is okay to handle this?? </div><div>BTW， as for the <span style="font-family:arial,sans-serif;font-size:14px">xtekct</span><span style="font-family:arial,sans-serif;font-size:14px"> file, file attached </span> is the geometry of Nikon H225 in the lab .</div><div><img src="cid:ii_149cf9207a4e90e9" alt="内嵌图片 1" width="472" height="318"><br></div><div><br></div><div>Best regards /谢谢您！</div><div>Guangming.</div><div class="gmail_extra"><div><div><div dir="ltr"><font style="line-height:23.3240013122559px" face="arial, helvetica, sans-serif" color="#674ea7"><b><i>Guangming Zang (Alex)</i></b></font><div style="line-height:23.3240013122559px"><font face="arial, helvetica, sans-serif"><b><i><font color="#0b5394">King Abdullah University of Science and Technology</font><font color="#073763">(KAUST)</font></i></b></font></div><div style="line-height:23.3240013122559px"><span style="font-family:arial;font-size:13px;line-height:20.0200004577637px"><font color="#0b5394"><b><i>University of Chinese Academy of Sciences(UCAS)</i></b></font></span><font face="arial, helvetica, sans-serif"><b><i><font color="#073763"><br></font></i></b></font></div><div style="line-height:23.3240013122559px"><br></div></div></div></div><div><div class="h5">
<br><div class="gmail_quote">2014-11-21 2:14 GMT+03:00 Chao Wu <span dir="ltr"><<a href="mailto:wuchao04@gmail.com" target="_blank">wuchao04@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Without more details I can only guess the meanings in your device xtekct file... suppose that the unit is mm.<div><br></div><div>Before anything, first check the resolution of your tiff files and see if it is 200 dpi.</div><div><br></div><div>Then try these geometry settings:<div><br><div><div>rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536</div><div>or</div><div><div>rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360 --arc=-360 --sdd=983 --sid=618.327880859375 --proj_iso_x=-121.666 --proj_iso_y=-97.536</div></div><div><br></div><div>Then for reconstruction:</div><div><br></div><div>rtksart -g My_geo2.xml -f CudaRayCast -b CudaVoxelBased -t 1 -p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension=1800,900,1800<br></div></div></div><div><br></div><div>No idea if these will work though...</div><div><br></div><div>Best regards,</div><div>Chao</div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div>2014-11-20 20:28 GMT+01:00 Guangming Zang <span dir="ltr"><<a href="mailto:guangming.zang@kaust.edu.sa" target="_blank">guangming.zang@kaust.edu.sa</a>></span>:<br></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div><div dir="ltr"><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif"> </span><span style="font-family:Cambria,serif;font-size:12pt">Hi Cyril,</span></p><p class="MsoNormal" style="margin-bottom:0.0001pt"><span style="font-size:12pt;font-family:Cambria,serif">It is so nice of you,
thanks for your very helpful help and reply. And thanks for introduction about the visualization tool ( VV ) . Yes,
actually, i want to use SART to reconstruct a whole volume. Considering that it
may be kind of time-consuming, so i just try to reconstruct one slice first.</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">And I want to use sart reconstruction algorithm from a series of
projections data scanned from Nikon XT H 225</span> (.tif format,360 projections and
360 arcs) . But when using sart, I am not sure about the geometry in our RTK
setting.</p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">File attached(two files) are the geometry information of object scanned and
360 projections, I used the command below, but I can not get the correct answer,
I think it is because my geometry’ setting is not correct, I used 2 commands:</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">Command 1 </span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">rtksimulatedgeometry.exe --output=My_geo2.xml --nproj=360
--arc=360 --sdd=983 --sid=618 --proj_iso_x=0 --proj_iso_y=-195</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">command 2</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">rtksart -g My_geo2.xml
-f CudaRayCast -b CudaVoxelBased -t 1
-p C:\Users\zangg\Desktop\Our_data\Toy -r .*.tif -o toy_cuda2.mha -n 3 --spacing=0.08 --dimension
150 150 100 </span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">In command 1, I am not sure about the proj_iso_x and proj_iso_y setting,
does it mean that the coordination of scanned object’s center map to the
projection? i used (0,-195) because in the geometry file (xml attached) the object coordination is(0,192,633.82) And the spacing setting as
the VoxelSize of x ,y,z. which is 0.07988 in xml.</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">In command 2 , I am not sure about the dimension and origin setting. I setting dimension as dimension(x,y,z)=
(VoxelSizeX*VoxelsX, VoxelSizeY*VoxelsY, VoxelSizeZ*VoxelsZ)< (150,150,100) </span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">And in sart options , I do not know how to set origin in my
case. So I just use defult value, but I think in my case, I should change the
value.</span></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px">in the xml file, i think maybe this may related to the origin setting</span></font></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px"> <VolumeOfInterest></span></font></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px"> <XStart>21</XStart></span></font></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px"> <XEnd>1757</XEnd></span></font></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px"> <YStart>108</YStart></span></font></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px"> <YEnd>1851</YEnd></span></font></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px"> <ZStart>293</ZStart></span></font></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px"> <ZEnd>1135</ZEnd></span></font></p><p class="MsoNormal"></p><p class="MsoNormal"><font face="Cambria, serif" size="3"><span style="line-height:18.3999996185303px"> </VolumeOfInterest></span></font></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">So can you help me to figure it out??</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">And , another question is, if I want to resize the projections(e.g,
from 2000*2000 to 500*500. How should I change my geometry setting in this case)???</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">Again, thanks and very grateful for your any help and
suggestion.</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">I am not sure if you can see the attached file, so if you want,
the 360 projections and geometry data are available at <span style="font-size:11pt;line-height:115%;color:rgb(34,34,34);text-decoration:none"><a href="https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing" target="_blank">https://drive.google.com/file/d/0B0W7oABtgSzXOWJyOWJDUVl6Ukk/view?usp=sharing</a></span></span><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif"></span></p><p class="MsoNormal"><span style="font-family:Cambria,serif;font-size:12pt;line-height:115%"> </span><span style="font-family:Cambria,serif;font-size:12pt;line-height:115%">The geometry only</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif"><span style="font-size:11pt;line-height:115%;color:rgb(34,34,34);text-decoration:none"><a href="https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing" target="_blank">https://drive.google.com/folderview?id=0B0W7oABtgSzXUjdVOS1uYldySDQ&usp=sharing</a></span></span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif"><br></span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">Thanks for you all, Cyril ,Simon and Chao</span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif"><br></span></p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">Best regards</span></p><span><font color="#888888"><p class="MsoNormal" style="margin-bottom:0.0001pt">
</p><p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:Cambria,serif">Guangming</span></p></font></span></div></div></div><div><div>
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